Fix issue in compare_folders

[thibaultdvx]

1. compare_folders used to not raise an error when it compared two empty directories. So, I added a check to make sure that the two directories to compare do exist. Consequently, I had to solve issues that appear in test_train_ae and test_predict with non existing folders.
2. I also made changes in test_predict.py and test_random_search.py because the flags introduced in Flag for local tests #608 didn't work well with these tests.
3. I also added indent in the json files stored in the temporary folders created by the tests.

This PR needs modifications in CI data: because of the bug spotted in 1., the tests of the test_train_ae pipeline used to pass, while some reference data are missing.

[thibaultdvx]

The tests were run with data in aramis-lab/clinicadl_data_ci#38

[camillebrianceau]

LGTM !